Clean topology with holes in a mesh with bevel modifier?
This is my way of making holes. It's probably not the best one, but looks good enough for me.

1) We subdivide a plane one time to many, and select 4 quads for each hole.



2) We do inset. (I)



3) We use Mesh: LoopTools add-on (just enable it) using Cicrcle tool.

(in edit mode right click and then LoopTools->Circle)



4) Inset one more time. (I)



5) Extrude downwards. (E)



6) Add Subdivision Surface modifier



7) Smooth shading (subdivided 2 times)



8) Render Eevee



To make hole sharper you can make more insets, and extrude down several times to put loop-cuts in all holes.